Cited by 602Genomics and Phylogenetic StudiesMicrobial Community Ecology and PhysiologyGut microbiota and health

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Current challenges and best-practice protocols for microbiome analysis

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Bharti, Richa, Grimm, Dominik G·2021·Briefings in Bioinformatics

DOI 10.1093/bib/bbz155PMC PMC7820839

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Abstract

Analyzing the microbiome of diverse species and environments using next-generation sequencing techniques has significantly enhanced our understanding on metabolic, physiological and ecological roles of environmental microorganisms. However, the analysis of the microbiome is affected by experimental conditions (e.g. sequencing errors and genomic repeats) and computationally intensive and cumbersome downstream analysis (e.g. quality control, assembly, binning and statistical analyses). Moreover, the introduction of new sequencing technologies and protocols led to a flood of new methodologies, which also have an immediate effect on the results of the analyses. The aim of this work is to review the most important workflows for 16S rRNA sequencing and shotgun and long-read metagenomics, as well as to provide best-practice protocols on experimental design, sample processing, sequencing, assembly, binning, annotation and visualization. To simplify and standardize the computational analysis, we provide a set of best-practice workflows for 16S rRNA and metagenomic sequencing data (available at https://github.com/grimmlab/MicrobiomeBestPracticeReview).

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Authors: Bharti, R., & Grimm, D. G.
Affiliations: Weihenstephan-Triesdorf University of Applied Sciences (DE)
Corresponding author: Grimm, Dominik G
ORCID: Bharti, Richa
Grimm, Dominik G
Venue: Briefings in Bioinformatics
Publisher: Oxford University Press (OUP)
Published: 2019-12-18
Volume: 22
Issue: 1
Pages: 178-193
ISSN: 1467-5463 (ISSN-L)
1477-4054
DOI: 10.1093/bib/bbz155
PMC: PMC7820839
OpenAlex: W2995649573
Cited by: 592
References: 184
Citations by year: 2026: 91 · 2025: 129 · 2024: 101 · 2023: 107 · 2022: 80 · 2021: 74 · 2020: 10
FWCI: 3.61
Type: journal article
Language: en
Open access: hybrid
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (vor)
Locations: Briefings in Bioinformatics (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
mediaTUM – the media and publications repository of the Technical University Munich (Technical University Munich) (submittedVersion)
mediaTUM – the media and publications repository of the Technical University Munich (Technical University Munich) (submittedVersion, other-oa)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Keywords: microbiome analysis, 16S rRNA gene sequencing, shotgun metagenomics, long-read metagenomics, best practice protocol, sample processing, sequencing quality control, metagenome assembly, metagenome binning, functional annotation, data visualization, experimental design
MeSH terms: Animals, Humans, RNA, Ribosomal, 16S, Practice Guidelines as Topic, Sequence Analysis, DNA, Metagenomics, DNA Barcoding, Taxonomic, Microbiota

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